A5065934968- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Developmental Biology and Gene Regulation
- RNA Research and Splicing
- Estrogen and related hormone effects
- RNA modifications and cancer
- Gene expression and cancer classification
- T-cell and B-cell Immunology
- Epigenetics and DNA Methylation
- Immunotherapy and Immune Responses
- Immune Response and Inflammation
- Gene Regulatory Network Analysis
- Genetics, Bioinformatics, and Biomedical Research
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Chromosomal and Genetic Variations
- Receptor Mechanisms and Signaling
- Molecular Biology Techniques and Applications
- Single-cell and spatial transcriptomics
- Immune cells in cancer
- Marine Ecology and Invasive Species
- Marine Invertebrate Physiology and Ecology
- Marine and coastal plant biology
- Planarian Biology and Electrostimulation
- Protist diversity and phylogeny
Université Paris Sciences et Lettres
2016-2025
Institut de Biologie de l'École Normale Supérieure
2016-2025
Inserm
2015-2025
École Normale Supérieure - PSL
2013-2025
Centre National de la Recherche Scientifique
2014-2025
École Normale Supérieure
2016-2025
Institut Français de Bioinformatique
2023
Institut Universitaire de France
2020-2021
Max Planck Society
2011-2013
Max Planck Institute for Molecular Genetics
2010-2013
RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cisregulatory elements in genome sequences.Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding (quality assessment, comparisons and clustering), (iii) comparative genomics (iv) regulatory variations.Nine new programs have been added 43 described 2011 NAR Web Software Issue, including tool extract sequences from list...
RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection cis-regulatory elements in genome sequences. Thirteen new programs have been added to 30 described 2008 NAR Web Software Issue, including an automated sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery algorithms (oligo-diff and info-gibbs), 100-times faster version matrix-scan enabling scanning genome-scale sets, series facilities random model generation...
ChIP-seq is increasingly used to characterize transcription factor binding and chromatin marks at a genomic scale. Various tools are now available extract motifs from peak data sets. However, most approaches only as command-line programs, or via website but with size restrictions. We present peak-motifs , computational pipeline that discovers in sequences, compares them databases, exports putative sites for visualization the UCSC genome browser generates an extensive report suited both naive...
RSAT (Regulatory Sequence Analysis Tools) is a suite of modular tools for the detection and analysis cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, including from genome-wide datasets like ChIP-seq/ATAC-seq, (ii) scanning, (iii) (quality assessment, comparisons clustering), (iv) regulatory variations, (v) comparative genomics. Six public servers jointly support 10 000 genomes all kingdoms. novel or refactored programs have been added since 2015...
RSAT (Regulatory Sequence Analysis Tools) enables the detection and analysis of cis-regulatory elements in genomic sequences. This software suite performs (i) de novo motif discovery (including from genome-wide datasets like ChIP-seq/ATAC-seq) (ii) sequences scanning with known motifs, (iii) (quality assessment, comparisons clustering), (iv) regulatory variations (v) comparative genomics. comprises 50 tools. Six public Web servers a teaching server) are offered to meet needs different...
Abstract Background Molecular and genetic analyses conducted in model organisms such as Drosophila vertebrates, have provided a wealth of information about how networks transcription factors control the proper development these species. Much less is known, however, evolutionary origin elaborated their large-scale evolution. Here we report first analysis whole superfamily factors, basic helix-loop-helix (bHLH) proteins, at scale metazoan kingdom. Results We identified silico putative full...
The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates wide collection of modular for the detection cis-regulatory elements in genome sequences.The includes programs retrieval, pattern discovery, phylogenetic footprint detection, matching, scanning and feature map drawing.Random controls can be performed with random gene selections or by generating sequences according to variety background models (Bernoulli, Markov).Beyond original...
The classical DNA recognition sequence of the glucocorticoid receptor (GR) appears to be present at only a fraction bound genomic regions. To identify sequences responsible for recruitment this transcription factor (TF) individual loci, we turned high-resolution ChIP-exo approach. We exploited signal by determining footprint profiles TF binding single-base-pair resolution using ExoProfiler, computational pipeline based on motifs. When applied our GR and few available public data sets, find...
Blood cells are derived from a common set of hematopoietic stem cells, which differentiate into more specific progenitors the myeloid and lymphoid lineages, ultimately leading to differentiated cells. This developmental process is controlled by complex regulatory network involving cytokines their receptors, transcription factors, chromatin remodelers. Using public data our own molecular genetic experiments (quantitative PCR, Western blot, EMSA) or genome-wide assays (RNA-sequencing,...
Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, which non-redundant collections are derived by manual curation. The advent high-throughput methods stimulated the production novel with increasing numbers motifs. Meta-databases, built merging these collections, redundant versions, because available tools not suited to automatically identify and explore biologically relevant clusters among thousands Motif discovery genome-scale data sets...
Position-specific scoring matrices (PSSMs) are routinely used to predict transcription factor (TF)-binding sites in genome sequences. However, their reliability novel binding can be far from optimum, due the use of a small number training or inappropriate choice parameters when building matrix scanning sequences with it. Measures quality such as E -value and information content rely on theoretical models, may fail context full We propose method, implemented program 'matrix-quality', that...
Abstract The glucocorticoid receptor (GR) binds as a homodimer to genomic response elements, which have particular sequence and shape characteristics. Here we show that the nucleotides directly flanking core-binding site, differ depending on strength of GR-dependent activation nearby genes. Our study indicates these change three-dimensional structure DNA-binding domain GR quaternary dimeric complex. Functional studies in defined context sequence-induced changes activity cannot be explained...
Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns the embryo. Among them are Hox genes, which define different identities along anterior–posterior axis. proteins exert their function by interaction with TALE transcription factors. and members also present some but not all non-bilaterian phyla, raising question how Hox–TALE interactions evolved to provide positional information. By using...
The genomic loci bound by the glucocorticoid receptor (GR), a hormone-activated transcription factor, show little overlap between cell types. To study role of chromatin and sequence in specifying where GR binds, we used Bayesian modeling within universe accessible chromatin. Taken together, our results uncovered that although preferentially binds chromatin, its binding is biased against located at promoter regions. This bias can only be explained partially presence fewer recognition...
CD4+ T cells recognize antigens through their cell receptors (TCRs); however, additional signals involving costimulatory receptors, for example, CD28, are required proper activation. Alternative have been proposed, including members of the Toll-like receptor (TLR) family, such as TLR5 and TLR2. To understand molecular mechanism underlying a potential role TLR5, we generated detailed maps logical models TCR signaling pathways merged model cross-interactions between two pathways. Furthermore,...
Significance For proteins to be able have context-specific activities, they can adopt conformations that enhance or restrict their activity. transcriptional regulatory factors, such a signal is provided by the sequence of DNA response element which it binds. Here we show how one signal, an alternative splicing event, rewires protein respond differently second binds, changing functional interplay between domains. Together, our findings argue bidirectional allosteric signaling DNA:protein...
The combination of long-read sequencing technologies like Oxford Nanopore with single-cell RNA (scRNAseq) assays enables the detailed exploration transcriptomic complexity, including isoform detection and quantification, by capturing full-length cDNAs. However, challenges remain, lack advanced simulation tools that can effectively mimic unique complexities scRNAseq datasets. Such are essential for evaluation optimization methods dedicated to long read studies. We developed AsaruSim, a...
Cellular differentiation is accompanied by dramatic changes in chromatin structure which direct the activation of lineage-specific transcriptional programs. Structure-specific recognition protein-1 (SSRP1) a histone chaperone important for chromatin-associated processes such as transcription, DNA replication and repair. Since function SSRP1 during cell remains unclear, we investigated its potential role controlling lineage determination. Depletion human mesenchymal stem cells elicited...
Precise patterns of gene expression are driven by interactions between transcription factors, regulatory DNA sequences, and chromatin. How mutations affecting any one these "layers" buffered or propagated to remains unclear. To address this, we quantified allele-specific changes in chromatin accessibility, histone modifications, F1 embryos generated from eight Drosophila crosses at three embryonic stages, yielding a comprehensive data set 240 samples spanning multiple layers. Genetic...